http://www.connectomeviewer.org/documentation/users/tutorials/tut_nbs.html
"""
title = ''
for idx, group_id in enumerate(group_list.keys()):
title += group_id
if not idx == len(group_list.keys()) - 1:
title += '-'
info = dict(dwi=[['subject_id', 'dti']],
bvecs=[['subject_id', 'bvecs']],
bvals=[['subject_id', 'bvals']])
l1pipeline = create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_dir, output_dir, info)
# Here with invert the b-vectors in the Y direction and set the maximum harmonic order of the
# spherical deconvolution step
l1pipeline.inputs.connectivity.mapping.fsl2mrtrix.invert_y = True
l1pipeline.inputs.connectivity.mapping.csdeconv.maximum_harmonic_order = 6
# Here we define the parcellation scheme and the number of tracks to produce
parcellation_name = 'scale500'
l1pipeline.inputs.connectivity.mapping.Parcellate.parcellation_name = parcellation_name
cmp_config = cmp.configuration.PipelineConfiguration()
cmp_config.parcellation_scheme = "Lausanne2008"
l1pipeline.inputs.connectivity.mapping.inputnode_within.resolution_network_file = cmp_config._get_lausanne_parcellation('Lausanne2008')[parcellation_name]['node_information_graphml']
l1pipeline.inputs.connectivity.mapping.probCSDstreamtrack.desired_number_of_tracks = 100000
l1pipeline.run()
http://www.connectomeviewer.org/documentation/users/tutorials/tut_nbs.html
"""
title = ''
for idx, group_id in enumerate(group_list.keys()):
title += group_id
if not idx == len(group_list.keys()) - 1:
title += '-'
info = dict(dwi=[['subject_id', 'dti']],
bvecs=[['subject_id', 'bvecs']],
bvals=[['subject_id', 'bvals']])
l1pipeline = create_group_connectivity_pipeline(group_list, group_id,
data_dir, subjects_dir,
output_dir, info)
# Here with invert the b-vectors in the Y direction and set the maximum harmonic order of the
# spherical deconvolution step
l1pipeline.inputs.connectivity.mapping.fsl2mrtrix.invert_y = True
l1pipeline.inputs.connectivity.mapping.csdeconv.maximum_harmonic_order = 6
# Here we define the parcellation scheme and the number of tracks to produce
parcellation_name = 'scale500'
l1pipeline.inputs.connectivity.mapping.Parcellate.parcellation_name = parcellation_name
cmp_config = cmp.configuration.PipelineConfiguration()
cmp_config.parcellation_scheme = "Lausanne2008"
l1pipeline.inputs.connectivity.mapping.inputnode_within.resolution_network_file = cmp_config._get_lausanne_parcellation(
'Lausanne2008')[parcellation_name]['node_information_graphml']
l1pipeline.inputs.connectivity.mapping.probCSDstreamtrack.desired_number_of_tracks = 100000